Ligand profile

ZINC113512038

Virtual-screening candidate from ZINC.

Bound to: VK055_4815 — lysine-arginine-ornithine-binding periplasmic family protein

Via homolog UniProt P35120 Formula C₉H₁₉N₃O₄
Tanimoto 0.64
Mol. weight 233.27 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC113512038
UniProt (similar protein)
P35120
Tanimoto
0.636
Target protein
VK055_4815

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 233.27 Da
LogP (Crippen) -0.86
H-bond donors 5
H-bond acceptors 5
TPSA 124.68 Ų
Rotatable bonds 9
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 0.78
Formula C₉H₁₉N₃O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 124.7
  • −1 ≤ LogP ≤ 5 -0.86
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 233.3
  • LogP ≤ 5 -0.86
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 124.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](NN[C@@H](CCCCN)C(=O)O)C(=O)O
InChI 
InChI=1S/C9H19N3O4/c1-6(8(13)14)11-12-7(9(15)16)4-2-3-5-10/h6-7,11-12H,2-5,10H2,1H3,(H,13,14)(H,15,16)/t6-,7-/m0/s1
InChIKey 
GZUNDMVLILFNOP-BQBZGAKWSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
AQQ
Homolog
P35120

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4815.

PDB 13

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)